NetPyNE 2021 Online Course
==========================

This courses introduces using NEURON via `NetPyNE <http://netpyne.org>`_,
a tool designed to simplify the construction, simulation, and analysis of
network models.

The first half of the course is mostly about NEURON, neuron theory, and relevant tools. NetPyNE-specific content begins in the second half of the course.

For those who prefer, this video series may also be accessed as a 
`YouTube playlist <https://www.youtube.com/watch?v=EP1pidV9luQ&list=PLrak8o3M0g0heH7Okr5Mf5s_Nu6hiCrja>`_. The playlist also includes guest speakers describing their research projects using NetPyNE and student project presentations.

Course introduction
-------------------

.. raw:: html

    <center><iframe width="560" height="315" src="https://www.youtube.com/embed/EP1pidV9luQ?rel=0" frameborder="0" allowfullscreen></iframe></center>


Single neuron theory I
----------------------

Bill Lytton, presenting.

.. raw:: html

    <center><iframe width="560" height="315" src="https://www.youtube.com/embed/PF09nEAzb1E?rel=0" frameborder="0" allowfullscreen></iframe></center>

General tech basics
-------------------

Topics:

- introduction to the terminal
- use of Google Colab and Jupyter notebooks

.. raw:: html

    <center><iframe width="560" height="315" src="https://www.youtube.com/embed/D-euIcEDX-o?rel=0" frameborder="0" allowfullscreen></iframe></center>

NEURON basics
-------------

Lecture
#######

.. raw:: html

    <center><iframe width="560" height="315" src="https://www.youtube.com/embed/sQje5YDirjY?rel=0" frameborder="0" allowfullscreen></iframe></center>


Exercises
#########

To facilitate interaction for the exercises, we split the class into two groups, taught by different people. The exercises are the same, however the discussions and details of the approaches vary.

Group 1
~~~~~~~

.. raw:: html

    <center><iframe width="560" height="315" src="https://www.youtube.com/embed/YOpIesuF7j8?rel=0" frameborder="0" allowfullscreen></iframe></center>


Group 2
~~~~~~~

.. raw:: html

    <center><iframe width="560" height="315" src="https://www.youtube.com/embed/PKnZCePJMXY?rel=0" frameborder="0" allowfullscreen></iframe></center>


Single neuron theory II
-----------------------

.. raw:: html

    <center><iframe width="560" height="315" src="https://www.youtube.com/embed/0Al8sJ4ZiE0?rel=0" frameborder="0" allowfullscreen></iframe></center>

.. _netpyne_neuron_rxd_video:

NEURON RxD
----------

Lecture
#######

.. raw:: html

    <center><iframe width="560" height="315" src="https://www.youtube.com/embed/UoQT5oXX08E?rel=0" frameborder="0" allowfullscreen></iframe></center>


Exercises
#########

To facilitate interaction for the exercises, we split the class into two groups, taught by different people. The exercises are the same, however the discussions and details of the approaches vary.

The three exercises:

- `pure diffusion <https://tinyurl.com/neuron-diffusion-exercise>`_
- `regenerative signaling <https://tinyurl.com/neuron-regen-signal>`_
- `Hodgkin-Huxley, concentrations, and homeostasis <https://tinyurl.com/neuron-hh-example-2>`_

Group 1
~~~~~~~

.. raw:: html

    <center><iframe width="560" height="315" src="https://www.youtube.com/embed/fD5ovL7OEVk?rel=0" frameborder="0" allowfullscreen></iframe></center>


Group 2
~~~~~~~

.. raw:: html

    <center><iframe width="560" height="315" src="https://www.youtube.com/embed/Lrf0EZAwLqk?rel=0" frameborder="0" allowfullscreen></iframe></center>


Network and synapse theory
--------------------------

Lecture
#######

.. raw:: html

    <center><iframe width="560" height="315" src="https://www.youtube.com/embed/OUqpCmpBnh0?rel=0" frameborder="0" allowfullscreen></iframe></center>


Networks in NEURON exercises
############################

.. raw:: html

    <center><iframe width="560" height="315" src="https://www.youtube.com/embed/j8Nv8uk1DWg?rel=0" frameborder="0" allowfullscreen></iframe></center>

NetPyNE GUI
-----------

Introduction
############

.. raw:: html

    <center><iframe width="560" height="315" src="https://www.youtube.com/embed/b_DpnRGmlHc?rel=0" frameborder="0" allowfullscreen></iframe></center>


Tutorials 1 and 2: Spinal cord
##############################

.. raw:: html

    <center><iframe width="560" height="315" src="https://www.youtube.com/embed/0utyHhLOa4s?rel=0" frameborder="0" allowfullscreen></iframe></center>


Tutorial 3
##########

.. raw:: html

    <center><iframe width="560" height="315" src="https://www.youtube.com/embed/hbCfBJapT58?rel=0" frameborder="0" allowfullscreen></iframe></center>

Tutorial 2: spinal cord
#######################

.. raw:: html

    <center><iframe width="560" height="315" src="https://www.youtube.com/embed/GXRYkF8q8vo?rel=0" frameborder="0" allowfullscreen></iframe></center>


Exercises
#########

.. raw:: html

    <center><iframe width="560" height="315" src="https://www.youtube.com/embed/HMhih84OV5I?rel=0" frameborder="0" allowfullscreen></iframe></center>

Tutorials 3-5
#############

.. raw:: html

    <center><iframe width="560" height="315" src="https://www.youtube.com/embed/rEQMHdBQn-8?rel=0" frameborder="0" allowfullscreen></iframe></center>

Tutorials 6 and 9
#################

.. raw:: html

    <center><iframe width="560" height="315" src="https://www.youtube.com/embed/Fcc-cg6t0Eg?rel=0" frameborder="0" allowfullscreen></iframe></center>

NetPyNE analysis and plotting
-----------------------------

.. raw:: html

    <center><iframe width="560" height="315" src="https://www.youtube.com/embed/x-uQcEx9yM8?rel=0" frameborder="0" allowfullscreen></iframe></center>

NetPyNE cell imports
--------------------

Lecture
#######

.. raw:: html

    <center><iframe width="560" height="315" src="https://www.youtube.com/embed/Md1K18vcjVc?rel=0" frameborder="0" allowfullscreen></iframe></center>


Hands-on
########

.. raw:: html

    <center><iframe width="560" height="315" src="https://www.youtube.com/embed/AbEEjeqr1a0?rel=0" frameborder="0" allowfullscreen></iframe></center>

Building data driven multiscale models
--------------------------------------

.. raw:: html

    <center><iframe width="560" height="315" src="https://www.youtube.com/embed/Zsx6GhKudLw?rel=0" frameborder="0" allowfullscreen></iframe></center>

Parameter exploration and optimization
--------------------------------------

Part 1
######

.. raw:: html

    <center><iframe width="560" height="315" src="https://www.youtube.com/embed/HYRdC42FcI8?rel=0" frameborder="0" allowfullscreen></iframe></center>

Part 2
######

.. raw:: html

    <center><iframe width="560" height="315" src="https://www.youtube.com/embed/mCVhegRDw80?rel=0" frameborder="0" allowfullscreen></iframe></center>

NetPyNE and RxD
---------------

.. raw:: html

    <center><iframe width="560" height="315" src="https://www.youtube.com/embed/KwRnIxAkNPw?rel=0" frameborder="0" allowfullscreen></iframe></center>

NetPyNE hands on batches
------------------------

.. raw:: html

    <center><iframe width="560" height="315" src="https://www.youtube.com/embed/EP1pidV9luQ?rel=0" frameborder="0" allowfullscreen></iframe></center>

NetPyNE virtual environments on mac and linux
---------------------------------------------

.. raw:: html

    <center><iframe width="560" height="315" src="https://www.youtube.com/embed/DU_yUJToH2E?rel=0" frameborder="0" allowfullscreen></iframe></center>
